Indexed on: 10 Feb '20Published on: 08 Feb '20Published in: Genome biology and evolution
The Candidate Phyla Radiation (CPR) is a proposed subdivision within the bacterial domain comprising of several candidate phyla. CPR microorganisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% new superfamilies to bacteria including the ribosomal protein L19e and encoded 4 core superfamilies that are likely involved in cell-to-cell interaction and establishing epi-symbiotic lifestyles. While CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial microorganisms that have probably evolved in an Archaea-like manner via the early loss of key metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2020. This work is written by US Government employees and is in the public domain in the US.